The use of lignin as a functional additive has long been a promising topic in both industry and academia, but the development of such systems is still limited by the considerable challenges posed by the incompatibility of lignin with common polymers. Herein, we designed modified silicone (MS) sealants with enhanced UV and thermal stability by incorporating molecularly engineered lignin bio-additives while establishing robust design principles to finely adjust the morphology of such blends by tailoring the molecular structures of lignin fractions. To that end, we first constructed a library of lignin fractions with various molecular weights (obtained by fractionating Kraft lignin and by using a lignin model compound) and with several chemical modifications (acetylation, butyrylation, and silylation). The lignin bio-additives were then melt-blended with MS polyethers. The experimental phase diagrams of the resulting blends were established and rationalized with a thermodynamic framework combining Hansen solubility parameters and Flory-Huggins theory, unraveling fascinating insights into the complex solubility behavior of lignin fractions and notably, for the first time, the subtle interplay between molecular weight (entropic effects) and chemical modifications (enthalpic effects). A molecularly optimized lignin additive was then selected to achieve full solubility while providing better thermal stability and UV-blocking properties to the resulting MS material. Overall, this article provides robust design principles for the elaboration of functional biomaterials with optimized morphologies based on rationally engineered lignin fractions.